Intraspecific fusion of protoplasts with nuclei in Antrodia cinnamomea lengthened the time for development of colonies on regeneration medium and reduced the number of protoplasts capable of regeneration. When 2.1×10^5 C98 protoplasts were fused with C96 nuclei, 1750 colonies appeared on the regeneration medium, and 742 of them were putative nuclear hybrids as their colonies were different from that of the protoplast parent. Without the presence of C96 nuclei, 3160 colonies appeared on the regeneration medium and 400 of them tested were similar to the protoplast parent in colony appearance. No colonies appeared when self-fused nuclei were plated on regeneration medium. The rate of successful transfer was 23%. The success rate was for reciprocal transfer. About 77 to 82% of nuclear hybrids were slow in growth. These isolates resumed normal growth upon subculture. All the nuclear hybrids obtained were unstable. Segregation occurred during growth of mycelia. resulting in the formation of colonies different from those of the originals in subcultures. After five consecutive subcultures, 13 stable nuclear hybrids were obtained. These isolates differed greatly from the parental isolates and from each other in pigmentation, growth rate, and colony pattern.